Today we begin our discussion of the
structure and properties of proteins.

Proteins consist in whole or large part of
amino acids.

Simple proteins consist only of amino
acids.

Conjugated proteins contain a non-amino
acid component called the prosthetic group.

The prosthetic group can be an organic or
an inorganic component such as a sugar
molecule or a metal ion.

Conjugated proteins are classified by the
prosthetic group.

Examples are nucleoproteins, lipoproteins
and metalloproteins which contain nucleic
acids, lipids and metal ions respectively.

There are approximately 20 different
amino acids found in proteins.

Most of the 20 common amino acids (a.a.)
have the following general structure-

The amino acids are distinguished from
each other by the R group often referred to as
the side-chain in proteins.

The a.a. have an amino and a carboxylic
acid group which are joined to the same carbon
atom. This carbon atom is referred to as the
carbon.

In proteins, amino acids are covalently
linked to one another by peptide (amide) bonds
involving the carboxyl group of one a.a. and the
amino group of another a.a. to form linear
polymers-

Let's examine the structure and properties
of the amino acids. The a.a. are usually
grouped according to the polarity and charge of
the R group which relates to their role in
proteins.

Table 4-1 places a.a. into three groups:
a.a. with nonpolar side chains, a.a. with
uncharged polar side chains and a.a. with
charged polar side chains.

Consider a.a. with nonpolar side chains.
This group includes the simplest a.a. glycine
whose R group is a H atom.

Most of the other a.a. in this group have
nonpolar alkyl or aromatic R groups. Alanine,
valine, leucine, isoleucine, and phenylalanine
have methyl, isopropyl, isobutyl, secondary
butyl and benzyl groups.

Methionine has a thioether group which is
nonpolar because the electronegativity of
sulfur is very similar to carbon.



Included in this group is the amino acid
proline which is a secondary a amino acid. The
N and carbon atoms are parts of a five
membered ring.

The a.a. tryptophan has a bicyclic ring
referred to as indole. Note that while the R
group appears to be relatively nonpolar, the N-
H group of indole is polar and can H-bond.

Most of the a.a. acids with uncharged polar
side chains have O and/or N atoms.

The side chains are polar because there is
a large difference in the electronegativities
of these atoms and the atoms to which they are
bonded. This difference contributes to an
unequal sharing of electrons in the bond which
results in a dipole.

Serine and threonine have hydroxyl groups.



Asparagine and glutamine have amide
groups as part of their side chains. They
differ from one another by a methylene, -CH₂-,
unit.

Tyrosine has a phenolic group.

Cysteine has a mercapto, -SH, group. The
mercapto group is only weakly polar.

The a.a. with charged polar side chains
have basic or acidic groups which are partly
or completely ionized at pH 7.0.

The basic a.a. include lysine, arginine and
histidine. Because they are basic, they will
associate with H⁺ in solution to form the
positively charged groups as shown in Table 4-
1 for lysine and arginine.

Lysine has an amino group on the (epsilon)
carbon atom.



The basic group of arginine is referred to
as the guanidino group-

The conjugate acid form shown in Table 4-
1 is called the guanidinium group-

The basic group of histidine is an imidazole
group.

The imidazole group of histidine is less
basic than the amino or guanidino group so that
at pH 7.0 it is predominately unprotonated as
shown in Table 4-1.

The acid form is called the imidazolium
group-



The acidic a.a. include aspartic and
glutamic acids which differ from one another
by a methylene unit.

Because the carboxylic acid groups are
acidic, they will dissociate to give a H⁺ and the
negatively charged carboxylate group at pH 7.0
as shown in Table 4-1.

Note that these groups are referred to as
the and carboxyl groups because they are
attached to the and carbon atoms.

Note that each a.a. has a 3 letter and a 1
letter abbreviation. This is useful in
representing the sequence of a.a. in a protein.